Evaluate gene sets by cell type-specific gene expression
Wei Sun
2024-07-04
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 3.00 23.00 24.00 23.73 25.00 27.00## [1] 40## [1] 3 20 21 21 22 22 22 23 23 23 23 24 24 24 24 24 24 24 24 24 24 25 25 25 25
## [26] 25 25 25 25 25 25 25 26 26 26 26 26 27 27 27Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"##
## FALSE TRUE
## 1607 42##
## FALSE TRUE <NA>
## 42 1565 42gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: C10orf91 LINC02870
## 2: C12orf10 MYG1
## 3: C12orf45 NOPCHAP1
## 4: C6orf48 SNHG32
## 5: C6orf99 LINC02901
## 6: CXorf40A EOLA1
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM173A ANTKMT
## 10: FAM213B PRXL2B
## 11: H2AFX H2AX
## 12: HIST1H2AG H2AC11
## 13: HIST1H2BK H2BC12
## 14: HIST1H2BN H2BC15
## 15: HIST1H3A H3C1
## 16: HIST1H3H H3C10
## 17: HIST1H4C H4C3
## 18: HIST2H2BF H2BC18
## 19: KIAA0391 PRORP
## 20: QARS EPRS1
## 21: SEPT6 SEPTIN6
## 22: ARNTL BMAL1
## 23: C12orf65 MTRFR
## 24: C16orf72 HAPSTR1
## 25: CCDC84 CENATAC
## 26: DOPEY2 DOP1B
## 27: FAM126B HYCC2
## 28: FAM160B1 FHIP2A
## 29: H1FX H1-10
## 30: H2AFJ H2AJ
## 31: HEXDC HEXD
## 32: HIST1H1C H1-2
## 33: HIST1H1D H1-3
## 34: HIST1H1E H1-4
## 35: KIAA1109 BLTP1
## 36: KIAA1551 RESF1
## 37: MKL1 MRTFA
## 38: NARFL CIAO3
## 39: SEPT2 SEPTIN6
## 40: TARSL2 TARS3
## 41: TMEM8A PGAP6
## 42: WDR60 DYNC2I1
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 1649 3## sym_in_data sym_limma gene_symbol
## 1: ABLIM1 ABLIM1 ABLIM1
## 2: AC004687.1 <NA> AC004687.1
## 3: AC004854.2 <NA> AC004854.2
## 4: AC007384.1 <NA> AC007384.1
## 5: AC007952.4 <NA> AC007952.4## t1
## 1 2
## 1647 1## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6Read in cell type-specific expression data
Cell type specific gene expression were downloaded from protein atlas.
## [1] 1587110 4## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5## [1] 79##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090## [1] 602700 5## Gene Gene name Immune cell TPM pTPM
## 1: ENSG00000000003 TSPAN6 basophil NA 1.2
## 2: ENSG00000000003 TSPAN6 Central memory CD8 T-cell NA 1.7
## 3: ENSG00000000003 TSPAN6 classical monocyte NA 0.2
## 4: ENSG00000000003 TSPAN6 Effector memory CD8 T-cell NA 0.7
## 5: ENSG00000000003 TSPAN6 Exhausted memory B-cell NA 0.7## Mode NA's
## logical 602700## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 0.00 3.10 49.74 27.20 96572.50## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.10 1.70 11.60 67.96 42.80 96572.50## [1] 30##
## basophil Central memory CD8 T-cell
## 20090 20090
## classical monocyte Effector memory CD8 T-cell
## 20090 20090
## Exhausted memory B-cell intermediate monocyte
## 20090 20090
## MAIT T-cell Memory CD4 T-cell TFH
## 20090 20090
## Memory CD4 T-cell Th1 Memory CD4 T-cell Th1/Th17
## 20090 20090
## Memory CD4 T-cell Th17 Memory CD4 T-cell Th2
## 20090 20090
## myeloid DC naive B-cell
## 20090 20090
## naive CD4 T-cell naive CD8 T-cell
## 20090 20090
## neutrophil NK-cell
## 20090 20090
## non-classical monocyte Non-switched memory B-cell
## 20090 20090
## Non-Vd2 gdTCR Plasmablast
## 20090 20090
## plasmacytoid DC Progenitor cell
## 20090 20090
## Switched memory B-cell T-reg
## 20090 20090
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell
## 20090 20090
## total PBMC Vd2 gdTCR
## 20090 20090## [1] 30 2## Cell_type Lineage
## 1: Basophil Granulocytes
## 2: Neutrophil GranulocytesCheck gene expression for each gene set
## [1] 1649 3for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct_immune$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct_immune[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Immune cell`) %in%
str_to_lower(lineage$Cell_type)))
mat1 = match(str_to_lower(df$`Immune cell`),
str_to_lower(lineage$Cell_type))
df = cbind(df, lineage[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
df = df[df$Lineage != "Total PBMC",]
df$Lineage = factor(df$Lineage,
levels = setdiff(lineage$Lineage, "Total PBMC"))
p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "AC008555.5" "AC012645.3" "AC044849.1" "AC087623.3" "AC119396.1"
## [6] "AC245297.3" "ARRDC2" "CCL4L2" "CLDND1" "CRLF3"
## [11] "EOMES" "HIKESHI" "INTS6L" "LINC00649" "PITPNC1"
## [16] "TRAV8-3" "TRGV7" "TRGV8" "ADGRG1" "ARHGAP30"
## [21] "CYTOR" "FCRL6" "NECAP1" "TTC38" "XCL2"
## [1] "found 16 genes."
## [1] 2
## [1] "AK5" "CHRM3-AS2" "COQ8A" "IGLV1-44" "LINC00402"
## [6] "LST1" "MATR3-1" "PDCD4-AS1" "RETREG1" "TC2N"
## [11] "TRAV14DV4" "TRAV8-2" "TRBV28" "TRBV9" "CLEC16A"
## [16] "DOCK10" "HIPK1" "HRH2" "IFI27" "NUTM2B-AS1"
## [21] "PIK3CD" "POLR2J3-1" "PPP4R3B" "PUM3" "S100A12"
## [26] "TUT4"
## [1] "found 20 genes."
## [1] 3
## [1] "NUAK2" "TBCCD1" "ABCA7" "ARHGAP10" "BTBD9" "DMTF1"
## [7] "ERBIN" "FAM126B" "FAM78A" "GK5" "HECA" "IRF9"
## [13] "MCTP2" "MYBL1" "MYO1F" "NFATC3" "NRDC" "OGA"
## [19] "PARP15" "PATL2" "PIK3R5" "RASGRP1" "RNF125" "SIDT1"
## [25] "TUT7" "XIST"
## [1] "found 24 genes."
## [1] 4
## [1] "CCR7" "FXYD7" "LTB" "SLC2A3" "AC016831.7"
## [6] "ARHGAP45" "ARHGEF9" "ATAD2B" "BMT2" "ETFDH"
## [11] "FAM133B" "GABPB2" "GPHN" "HPS4" "KAT6B"
## [16] "LINC02446" "MARF1" "OXNAD1" "PCED1B" "PNPLA8"
## [21] "PSMA3-AS1" "RIPOR2" "SEC14L1" "THAP5" "TMEM131L"
## [26] "ZNF83"
## [1] "found 23 genes."
## [1] 6
## [1] "HLA-DMB" "KLRB1" "KLRC3" "KLRK1" "MAN2B1" "OXA1L"
## [7] "TFB2M" "TIGIT" "CMKLR1" "CSNK1G2" "GALNT10" "GDPD5"
## [13] "ITGAM" "KIR2DL3" "RAPGEF1" "SLC20A1" "SLC38A10" "TIMP1"
## [19] "TMEM127" "TMEM181" "TMEM8A" "TTC17"
## [1] "found 22 genes."
## [1] 7
## [1] "CCNB1IP1" "ADGRE5" "ARL4C" "CARD11" "CARD16" "CD52"
## [7] "CTSW" "CX3CR1" "DDX60L" "IFITM2" "ITM2A" "KDM3B"
## [13] "KIAA1551" "LAG3" "LY6E" "MT2A" "MYO1G" "RALGAPB"
## [19] "S100A11" "TRAC" "TRAV12-3" "TRAV17" "TRAV9-2" "TRBV11-2"
## [25] "TRGC2" "ZNF683"
## [1] "found 24 genes."
## [1] 8
## [1] "AIF1" "CHMP1B" "NSUN6" "CASP10" "CAST" "CCDC88C" "CD46"
## [8] "CELF2" "CFLAR" "DDHD1" "DENND6A" "ITK" "KCNAB2" "KDM5A"
## [15] "KLF3" "LRBA" "MTMR6" "NCKAP1L" "PCYT1A" "PRKCH" "RASA3"
## [22] "RIC3" "SPG11" "WDR7"
## [1] "found 24 genes."
## [1] 9
## [1] "ID2" "ISCA1" "MAP3K2" "MSC" "NDE1" "SPECC1" "ABHD17A"
## [8] "BHLHE40" "DOCK11" "EFHD2" "FRYL" "GSE1" "LENG8" "MACF1"
## [15] "MAP3K3" "PHF3" "PLEKHG3" "POLH" "PRR5L" "PTPN23" "SSH1"
## [22] "STK38" "WAC" "ZFYVE16"
## [1] "found 24 genes."
## [1] 10
## [1] "CD27" "CPNE1" "CREBL2" "CYB561A3" "EPB41L4A-AS1"
## [6] "FCER1G" "IER3" "ITGAE" "KIR3DL2" "LRRC23"
## [11] "NCR1" "NR4A3" "NT5DC1" "SDR42E2" "SLC38A1"
## [16] "TMEM107" "TMEM204" "TMEM42" "TSPYL4" "UIMC1"
## [21] "ZFAND1" "PARP4" "TEP1" "TRIM38"
## [1] "found 23 genes."
## [1] 11
## [1] "GLA" "MAT2B" "ARHGEF3" "ARID5B" "BROX" "CAPNS1" "GCN1"
## [8] "GPRIN3" "IL2RG" "INO80D" "KLF2" "KLF6" "NCOA7" "NLRC5"
## [15] "PLA2G6" "PLAC8" "SENP7" "SLFN12L" "STK17B" "TOB1" "USP16"
## [22] "XAF1" "ZBP1" "ZBTB20" "ZDHHC20"
## [1] "found 25 genes."
## [1] 12
## [1] "THAP9-AS1" "AKNA" "AP005482.1" "CEMIP2" "DIAPH2"
## [6] "GPR174" "LINC02384" "MIAT" "MX2" "NBEAL2"
## [11] "OAS2" "ODF3B" "PCSK7" "SAMD9L" "TBC1D14"
## [16] "THUMPD3-AS1" "TRANK1" "TRAPPC11" "TRAPPC8" "TRAV19"
## [21] "TRAV27" "TRAV4" "TRBV2" "TRDV1" "TRGV10"
## [26] "TRGV4" "TSPAN32"
## [1] "found 22 genes."
## [1] 13
## [1] "AC083798.2" "AL121944.1" "ARMH1" "ATP2B1-AS1" "BBS9"
## [6] "FAM213B" "IGKV3-20" "INPP4B" "LRRN3" "NPIPB4"
## [11] "NUP58" "PRAG1" "RAB33B" "SLC27A5" "TNFRSF25"
## [16] "TRABD2A" "TRAV12-2" "TRAV5" "TRAV8-4" "TRBV3-1"
## [21] "TRBV6-1" "TRBV6-2" "ZNF749" "ZNF862" "MTERF2"
## [26] "RUFY2" "SLCO3A1"
## [1] "found 24 genes."
## [1] 14
## [1] "AC007384.1" "AC020911.2" "AC025171.3" "AC083880.1" "AC091271.1"
## [6] "AC103591.3" "AF213884.3" "AL139246.5" "AL357060.1" "AL451085.1"
## [11] "AL627171.1" "ASL" "C6orf99" "HELQ" "HIPK1-AS1"
## [16] "IFRD1" "KCNQ1OT1" "LINC01465" "MZF1-AS1" "NT5C3B"
## [21] "OSER1-DT" "PGGHG" "RGS1" "TRAV3" "TRBV7-9"
## [26] "C16orf72" "HIVEP3"
## [1] "found 9 genes."
## [1] 15
## [1] "ACTR1B" "C12orf10" "EIF1" "EIF2S3" "EIF3E" "EIF3G"
## [7] "EIF3K" "EIF3L" "EIF4A2" "PAIP2" "PHLDA1" "RACK1"
## [13] "ATAD2" "DDX60" "EIF3A" "EIF4G1" "EIF4G3" "LRRFIP1"
## [19] "MSI2" "PRRC2C" "SECISBP2"
## [1] "found 21 genes."
## [1] 16
## [1] "AC004687.1" "AC087239.1" "AL118516.1" "AL138963.3" "ANXA2R"
## [6] "ATP5F1A" "BTG2" "CCNI" "CMC1" "FCMR"
## [11] "GCSAM" "GTF3A" "ICAM3" "KLRF1" "MFNG"
## [16] "NBPF14" "NOP53" "PPP1R15B" "PRR7" "RTRAF"
## [21] "SNHG15" "SNHG9" "TRG-AS1" "WDR86" "WSB1"
## [26] "ZNF276"
## [1] "found 19 genes."
## [1] 17
## [1] "ARL4A" "IL6R" "RGCC" "TXK" "UBL7" "ZC3H12A" "ZNF10"
## [8] "CLUH" "COX19" "ELMO1" "ETV6" "GON4L" "LONP2" "NAA25"
## [15] "NFKBIZ" "PARP14" "PARP9" "PDE4B" "PHF14" "PIGF" "SETD2"
## [22] "USP34" "WDR37" "ZNF557"
## [1] "found 24 genes."
## [1] 18
## [1] "AKTIP" "GLS" "HIST1H2BK" "HIST1H2BN" "IL16" "NCF1"
## [7] "PPA1" "SSR2" "TBC1D17" "BDP1" "CPT1A" "CYBA"
## [13] "DHX29" "FGR" "NEMF" "NNT" "PKD1" "PPP1R12C"
## [19] "PTMS" "UPF2"
## [1] "found 20 genes."
## [1] 19
## [1] "ASAH1" "ATP5MG" "CD7" "GATA3" "GRAMD1A" "MZT2A"
## [7] "MZT2B" "PNRC1" "PPP1R15A" "PTGER4" "VAMP7" "CD99"
## [13] "DNAJB14" "KLHDC4" "NUP210" "PTPN4" "PTPN7" "RORA"
## [19] "ST6GAL1" "TBX21" "TUBGCP6" "ZFAND3"
## [1] "found 22 genes."
## [1] 20
## [1] "ARHGAP9" "C12orf45" "CXXC5" "EI24" "GIMAP1" "GPR183"
## [7] "GSTM1" "GSTM4" "LCP2" "LETMD1" "PCMTD2" "PDE7A"
## [13] "RTN3" "SESN2" "TRAT1" "ARAP2" "FAM169A" "LRRC8A"
## [19] "MCOLN2" "MICAL2" "SZT2" "VPS13A" "VPS13D"
## [1] "found 22 genes."
## [1] 21
## [1] "CAMK4" "CMTM7" "EPHX2" "EPS8" "FAM102A" "HIBADH"
## [7] "LDLRAP1" "NOSIP" "RCAN3" "SELL" "STMN3" "TCEA3"
## [13] "TCF7" "TESPA1" "TRAV21" "ZNF575" "GPANK1" "HERC3"
## [19] "HERC6" "ITPR2" "MAPK8IP3" "SCRN3" "SOS1" "VCAN"
## [25] "ZNF493"
## [1] "found 24 genes."
## [1] 22
## [1] "AMD1" "C12orf57" "CD84" "DTHD1" "FAM118A" "GLTP"
## [7] "GZMK" "KLRG1" "NOCT" "PIK3IP1" "RCSD1" "RGL4"
## [13] "RSRP1" "SH2D1A" "SLC38A2" "STK17A" "TOX" "TRBC1"
## [19] "TRGV5" "WARS2" "CCDC112" "ERAP2" "SLK" "VPS13B"
## [25] "YPEL1"
## [1] "found 25 genes."
## [1] 23
## [1] "ALOX5AP" "APMAP" "HDHD3" "LAPTM5" "LBH" "LIME1" "MATK"
## [8] "PTPRCAP" "PTRHD1" "RHOC" "THEM4" "TMEM134" "CBX7" "CST7"
## [15] "FGFBP2" "GZMA" "GZMB" "NKG7" "PHC3" "PLEK" "SPON2"
## [22] "SRGN" "UBE4A" "UCP2"
## [1] "found 24 genes."
## [1] 24
## [1] "NT5E" "SNRPN" "ZEB1" "AFF1" "AFF4" "ARID1A" "ARID1B"
## [8] "BAZ2A" "CHD1" "CRNKL1" "DGKD" "NKTR" "PIP4K2B" "PNN"
## [15] "PPIG" "RNF157" "RNMT" "RNPC3" "SCAF8" "SMG1" "USP42"
## [22] "WDR60"
## [1] "found 22 genes."
## [1] 25
## [1] "BTG1" "FOXP1" "KLHDC2" "PPP1R10" "PRPF38B" "SAT1"
## [7] "SATB1" "ZBTB10" "ARHGAP4" "ASH1L" "FAM160B1" "HERC1"
## [13] "MALAT1" "MORC3" "NEAT1" "RUNX3" "SLTM" "TCF25"
## [19] "TFDP2" "TTF2" "ZC3H7B" "ZEB2" "ZNF335"
## [1] "found 20 genes."
## [1] 26
## [1] "AC004854.2" "AC015982.1" "AC016405.3" "AC027644.3" "AOAH"
## [6] "ARF4-AS1" "BX284668.6" "CRTAM" "CSKMT" "CXorf40A"
## [11] "IER5" "ILF3-DT" "KLF10" "KMT2E-AS1" "MAPRE2"
## [16] "MTRNR2L8" "PAPSS1" "SLC4A4" "TRAV38-2DV8" "TRBV6-5"
## [21] "TRBV7-2" "TRGV9" "Z93241.1" "GALNT3" "RLF"
## [1] "found 16 genes."
## [1] 27
## [1] "HMGCS1" "RELT" "TPRKB" "CAPN15" "DNAJC13" "EPSTI1"
## [7] "GPATCH2L" "HSH2D" "IFI44" "IFI44L" "IGHA1" "IGKC"
## [13] "MBD5" "MX1" "PHF11" "PPM1K" "PRKX" "PTPRJ"
## [19] "RNF213" "S100A8" "SPOCK2" "STK10" "TTC14"
## [1] "found 23 genes."
## [1] 28
## [1] "LPXN" "C2CD3" "CEP164" "CEP350" "CTDSPL2" "DENND4C" "ENTPD4"
## [8] "GIGYF1" "HELZ2" "HIPK3" "IFIT2" "IFIT3" "KIF13B" "LIMD1"
## [15] "MAN2C1" "N4BP1" "PHACTR4" "PSTPIP2" "REXO1" "RIF1" "SMCHD1"
## [22] "ZCCHC2" "ZNF292" "ZNF800"
## [1] "found 24 genes."
## [1] 29
## [1] "CST3" "CYB5D2" "GALNT11" "INTS8" "PDE3B" "SAE1"
## [7] "ADAM10" "AHCTF1" "ASCL2" "CHST12" "CTSC" "DOPEY2"
## [13] "FAR1" "GALNT2" "HLA-DQA1" "HLA-DRB1" "KLRD1" "LILRB1"
## [19] "LPCAT1" "MPPE1" "MYO9B" "PDE12" "PNPLA6" "PRF1"
## [1] "found 24 genes."
## [1] 30
## [1] "ABCC10" "AC092683.1" "AC116407.2" "ADCY7" "AP3M2"
## [6] "CCDC84" "CREBZF" "ELMOD3" "GPR132" "GRK2"
## [11] "IGKV3-15" "LINC02256" "MIGA1" "PCNX1" "RUBCN"
## [16] "SLF2" "SPATA13" "TENT5C" "TRBV4-2" "TRBV7-6"
## [21] "TTTY15" "UTY" "Z93930.2" "ZNF652" "ZNF808"
## [1] "found 20 genes."
## [1] 31
## [1] "COMMD6" "COTL1" "RPL41" "TOMM7" "TPGS2" "TRAF3IP2"
## [7] "YPEL3" "ARHGAP35" "B2M" "CD8A" "CD8B" "FNDC3B"
## [13] "GCA" "HEXDC" "KIAA0232" "LSS" "MKL1" "OAS3"
## [19] "POLG" "PRSS23" "SBK1" "TAF1D" "TMSB10" "TMSB4X"
## [1] "found 24 genes."
## [1] 32
## [1] "CD28" "TLE4" "ARAP1" "C5orf24" "CCL4" "CES1"
## [7] "CROCC" "ETNK1" "GNLY" "GNPTAB" "GPR141" "INPP5D"
## [13] "KIAA2026" "MKLN1" "NARFL" "PDZD4" "PEX1" "PEX26"
## [19] "SEMA4D" "ST8SIA4" "SUSD1" "SYNE1" "UBR2" "WDTC1"
## [25] "YPEL5"
## [1] "found 25 genes."
## [1] 33
## [1] "FCRL3" "ITGB1BP1" "ANKRD12" "APOL6" "BTN3A1" "CCNH"
## [7] "CD38" "EML4" "ERICH1" "FAM13B" "ITGAL" "PREX1"
## [13] "PYROXD1" "RHOH" "SLA2" "SLC35F5" "SLFN5" "STAT4"
## [19] "SYNRG" "TAOK1" "TAOK3" "TIPARP" "TRBC2" "UNC13D"
## [25] "ZAP70"
## [1] "found 25 genes."
## [1] 34
## [1] "AC025164.1" "AL135791.1" "ALKBH7" "BEX4" "BNIP3L"
## [6] "C6orf48" "CD40LG" "COA1" "HIST1H3H" "JAML"
## [11] "LINC02273" "MCUB" "MYLIP" "NR1D1" "SESN1"
## [16] "SNHG12" "TMIGD2" "TRAV1-2" "TRAV13-1" "TRBV20-1"
## [21] "CISH" "CRYBG1" "R3HCC1L" "RFWD3" "SETX"
## [1] "found 20 genes."
## [1] 35
## [1] "AC007952.4" "AC245014.3" "CITED2" "COQ7" "CSRNP1"
## [6] "DYRK4" "EFCAB2" "FAM173A" "GADD45B" "GLRX5"
## [11] "IER2" "KCTD7" "MPST" "MZF1" "NELL2"
## [16] "NR4A2" "TCP11L2" "TGIF1" "ZFAS1" "ZFP36L1"
## [21] "LTBP4" "PRR14L" "SETD5" "ZBTB40"
## [1] "found 21 genes."
## [1] 36
## [1] "C10orf91" "AC020659.1" "ANKRD36B" "ANKRD36C" "BICRAL"
## [6] "CHD9" "COL6A2" "COL6A3" "CPPED1" "DENND4B"
## [11] "EHBP1L1" "IQCG" "LAIR2" "MINDY2" "NLRC3"
## [16] "RAB27B" "RNF19A" "SLC16A1-AS1" "SYTL3" "TRDC"
## [21] "TTC16" "VPS13C" "VTI1A" "XCL1" "ZNF708"
## [1] "found 22 genes."
## [1] 37
## [1] "BACH2" "EGR1" "FOSB" "HIST1H4C" "JUNB" "MAF1"
## [7] "NUCB2" "RGS10" "RPL22L1" "SEPT6" "SNHG8" "TSR3"
## [13] "ACAP3" "ARRDC3" "CYTH1" "FOSL2" "JUND" "L3HYPDH"
## [19] "MAF" "MIDN" "POLR3D"
## [1] "found 20 genes."
## [1] 38
## [1] "CD83" "COG5" "HMBOX1" "IKZF2" "KIF9" "NXT2"
## [7] "ANKRD36" "ANKRD49" "BCL9L" "CD226" "COG7" "FNBP1"
## [13] "INPP4A" "IRAK4" "PPP1R16B" "RAP1GAP2" "SPN" "SSBP3"
## [19] "THADA" "UVRAG" "VPS18" "VPS39" "XPO6"
## [1] "found 23 genes."
## [1] 39
## [1] "AL136454.1" "SERINC5" "ABCA5" "ADHFE1" "CHD6"
## [6] "DDIT4" "DDX3Y" "DUS1L" "EIF1AY" "ENOSF1"
## [11] "FGL2" "GBP5" "HECTD4" "ISG20" "KDM5D"
## [16] "KIAA1109" "LPIN1" "OSM" "PARP11" "RPS4Y1"
## [21] "SBNO2" "SUSD6" "TARSL2" "ZMIZ2" "ZNF236"
## [1] "found 23 genes."
## [1] 40
## [1] "CXorf57" "ID1" "PLK2" "SBF2" "ABR" "ANKRD44" "EHD4"
## [8] "EIF4E3" "FAM53B" "H6PD" "MYOM2" "NEK9" "NRDE2" "PPIL2"
## [15] "PRDM2" "PTGDS" "RBSN" "RREB1" "SBF1" "TBC1D2B" "TMX3"
## [22] "UQCC2" "ZNF407" "ZNF827"
## [1] "found 24 genes."
Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4190026 223.8 11673970 623.5 NA 11673970 623.5
## Vcells 20600971 157.2 61723001 471.0 65536 61693859 470.7## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5